dbSNP rs17816376: PEX11A:c.56+255A>G (chr15-89690322-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003847.3(PEX11A):c.56+255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,186 control chromosomes in the GnomAD database, including 2,604 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2604 hom., cov: 32)

Consequence

PEX11A
NM_003847.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

12 publications found

Variant links:

Genes affected

PEX11A (HGNC:8852): (peroxisomal biogenesis factor 11 alpha) This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

PEX11A links:

WDR93 (HGNC:26924): (WD repeat domain 93) Predicted to enable oxidoreductase activity, acting on NAD(P)H. Predicted to be involved in electron transport chain. Predicted to be part of mitochondrial respiratory chain complex I. [provided by Alliance of Genome Resources, Apr 2022]

WDR93 Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

WDR93 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PEX11A	NM_003847.3 link	c.56+255A>G	intron_variant	Intron 1 of 2	ENST00000300056.8	NP_003838.1	O75192-1B2R8C6
PEX11A	NM_001271572.2 link	c.56+255A>G	intron_variant	Intron 1 of 2		NP_001258501.1	O75192-2B2R8C6
PEX11A	NM_001271573.2 link	c.-264+255A>G	intron_variant	Intron 1 of 1		NP_001258502.1	B2R8C6B4DMF6
WDR93	XM_011521794.3 link	c.-132T>C	upstream_gene_variant			XP_011520096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEX11A	ENST00000300056.8 link	c.56+255A>G		intron_variant	Intron 1 of 2	1	NM_003847.3	ENSP00000300056.3		O75192-1

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27132

AN:

152068

Hom.:

2605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.178

AC:

27131

AN:

152186

Hom.:

2604

Cov.:

AF XY:

0.176

AC XY:

13073

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.161

AC:

6678

AN:

41542

American (AMR)

AF:

0.143

AC:

2192

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

814

AN:

3466

East Asian (EAS)

AF:

0.00174

AC:

AN:

5176

South Asian (SAS)

AF:

0.215

AC:

1033

AN:

4812

European-Finnish (FIN)

AF:

0.182

AC:

1934

AN:

10600

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.205

AC:

13945

AN:

67988

Other (OTH)

AF:

0.191

AC:

403

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1193

2387

3580

4774

5967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.199

Hom.:

8926

Bravo

AF:

0.174

Asia WGS

AF:

0.0920

AC:

322

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.7

(source)

DANN

Benign

0.40

PhyloP100

-1.4

PromoterAI

-0.016

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over